OUR TEAM

LAB 2 WRITE-UP

Thermal Cycler Engineering

Our re-design is based upon the Open PCR system originally designed by Josh Perfetto and Tito Jankowski.

System Design

Key Features

There are two specific features that will be upgraded in the OpenPCR machine - the case and the power source. The case will be changed from a thin wood to a more durable plastic, so that the device can be taken out into the field. The device will also have solar panels, which will provide for the power. This shift allows the device to be used where electricity is not always available, such as rural and undeveloped regions. When combined, these two features open the device up to a larger market.

Instructions

The instructions would remain the same, as the solar panel array would come attached to the plastic on the device's top side.

Protocols

Materials

Supplied in Kit

Item

Quantity

PCR Machine

1 unit

Camera Phone Stand

1 unit

Fluorimeter Stand (LED Light)

1 unit

BlackOut Box

1 unit

Operator's Manual

1 unit

Also included: Access code for smart phone app download.

Supplied by User

Item

Quantity

Smart Phone (w/ Camera)

1 unit

USB/Phone Cord (if desired)

1 unit

Micropipettes

(as needed)

Hydrophobic Glass Slides

(as needed)

Eppendorf Tubes

Max 16 tubes/trial

Sample DNA

0.2μL/tube; 16 tubes/trial

GoTAQ Master Mix

50μL/tube; 16 tubes/trial

10 μM Forward Primer

1μL/tube; 16 tubes/trial

10 μM Reverse Primer

1μL/tube; 16 tubes/trial

Distilled H2O

47.8μL/tube; 16 tubes/trial

SYBR Green

0.1mL/test sample

PCR Protocol
1.) Be sure to be in an area with natural lighting for use of the solar battery, or locate an area with a standard power source availible
2.) Connect the PCR machine via USB to the computer
4.)
DNA Measurement Protocol

Research and Development

Background on Disease Markers

The disease that we chose was Sickle Cell Anemia. Sickle Cell is a inherited disease that comes from both parents. If only one parent has the Sickle Cell trait, then the child will be a carrier. If both parents have the trait, then the child will have Sickle Cell. This disease causes the red blood cells to change into a crescent shape instead of being disk shape resulting in the loss of efficient oxygen delivery. It can also result in clotting because the blood cells can not make it through small blood vessels very well. The SNP for this disease is 78478128 and the reference SNP is rs78478128.

The reverse primer for Sickle Cell is 5'-gaattcgtctgtttcccattctaaac-3'

The mutation looks like this: TCCTGAGGAG with the bold a being the mutation.

A disease allele will give a PCR result and a non-disease allele will not because PCR is designed to amplify the area that corresponds to the mutation on the DNA. If it did not amplify only the target region, there would be too much information and a result would not be possible.